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United States Department of Agriculture

Agricultural Research Service

Research Project: Conservation, Genetic Analyses, and Utilization of Subtropical/Tropical Fruit Crops, Sugarcane, and Miscanthus Genetic Resources

Location: Subtropical Horticulture Research

Title: Impact Of Selfing On The Inference Of Demographic History From Whole Genomes In Theobroma cacao L.

item Cornejo, Omar
item Kuhn, David
item Livingstone Iii, Donald
item Mockaitis, Keithanne
item Royaert, Stefan
item Findley, Seth
item Mustiga, Guiliana
item Schnell, Raymond
item Bustamante, Carlos
item Motamayor Arias, Juan Carlos

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2013
Publication Date: 1/13/2013
Citation: Cornejo, O., Kuhn, D.N., Livingstone Iii, D.S., Mockaitis, K., Royaert, S., Findley, S.D., Mustiga, G., Schnell, R.J., Bustamante, C., Motamayor Arias, J. 2013. Impact Of Selfing On The Inference Of Demographic History From Whole Genomes In Theobroma cacao L.. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.

Interpretive Summary:

Technical Abstract: Theobroma cacao L (cacao: Malvaceae) is a small tree found naturally in the Amazonian rain forest. An interesting feature of cacao is that it persists in populations of naturally outcrossing and inbreeding plants, as it is a species with a complex system of self-incompatibility, where a fraction of the population is able to undergo the most extreme form of inbreeding: self-fertilization. The theoretical consequences of inbreeding have been well characterized by theoretical population genetic studies; in particular the reduction in heterozygosity caused by self-fertilization and the fitness decrease in highly inbreed individuals in the population. A less trivial result, also derived from theoretical analyses, is the impact of selfing on the inference of demographic history from genetic data. Theoretical results have shown that inbreeding only increases the probability of coalescence between alleles found within a single diploid individual; with little impact on the estimation of the coalescent process as a whole. In this work, we show improved estimates of the demographic history of cacao, by including a larger number of sequenced accessions, and evaluate the impact of selfing in the estimation of the demographic history of cacao. Our estimates of inbreeding, from microsatellite data, suggest that different populations undergo different selfing rates that vary from 0.25 to 0.9, consistent with the range of inbreeding coefficients (F) estimated from individually sequenced genomes. We use forward simulations to estimate in a maximum likelihood framework the demographic history of cacao, and evaluate with the aid of simulations the impact of selfing on our estimations.

Last Modified: 10/17/2017
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